GCC 2017

➔ Slides

Authors

Pratik Jagtap, University of Minnesota (Galaxy-P)
Björn Grüning, University of Freiburg
James Johnson, University of Minnesota
Alessandro Tanca, Porto Conte Ricerche
Bart Mesuere, Ghent University
Judson Hervey, Naval Research Laboratory
Carolin Kolmeder, University of Helsinki
Jeremy Fischer, Indiana University
Thomas Doak, Indiana University
Thilo Muth, Robert Koch Insitute Berlin
Dave Clements, Johns Hopkins University
Praveen Kumar, University of Minnesota
Subina Mehta, University of Minnesota
Thomas McGoan, University of Minnesota
Clemens Blank, University of Freiburg
Bernhard Renard, Robert Koch Insitute Berlin
Josh Elias, Stanford University
Joel Rudney, University of Minnesota 
Timothy Griffin, University of Mineesota


Abstract
The impact of microbial gene expression (‘microbiome') on human health and environment is receiving increased attention, mostly by applying gene-centric metagenomics analytical approaches. As genes can only reveal potential functions, the characterization via metaproteomics analysis (study of expressed microbial proteins) may reveal the mechanism of microbial responses in ecosystems. However, computational metaproteomics needs deliberate, international coordination to generate robust and sustainable software that can contribute to advance metaproteomics research.

Researchers on this project are metaproteomics informatics developers and users who communicate via mailing list, gitter, and GitHub to jointly define and develop the most useful tools to enable metaproteomics analysis. In December 2016, the researchers held an online Metaproteomics Contribution Fest to develop and implement metaproteomics-focused software tools. Prioritization of tasks resulted in identification of the following tool categories within the complex metaproteomics analytical pipeline:

1) Database generation tools using results from the 16S rRNA data/approach to define taxonomy lists and shotgun metagenome sequencing data (May et al J Proteome Res. 15:2697).

2) Peptide spectral matching tools such as SearchGUI /PeptideShaker and post-processing by MetaProteomeAnalyzer.

3) Taxonomic classification and functional characterization using UniPept and packaging and testing of DIAMOND to generate outputs for MEGAN analysis.

These developed tools are being made accessible through the Galaxy Toolshed and a publicly available metaproteomics gateway at NCGAS. Vetted tools and workflows are accessible and will be updated and tested on this Jetstream cloud computing infrastructure.

Our tools, workflows and resources are being promoted via publications, presentations and training workshops at scientific conferences.